Additional file 2 of The Local Edge Machine: inference of dynamic models of gene regulation

Table: Biological prior information about gene function used for LEM inference on yeast cell-cycle networks 1–5. LEM can incorporate biological priors to remove any impossible edges (e.g., a TF known to be an activator cannot repress a given target), which improves inference on real data (see Additional files 5 and 13). Here we provide literature evidence for TFs that function as an activator of target gene transcription, repressor, or both. Genes marked N/A do not function as TFs. Note 1. CLN3 is included as a regulator in networks 1, 2, and 5 because it is known to inhibit Whi5 at cell-cycle START [2]. The other cyclins, CLN2 and CLB2, are not included as regulators because their effects on TFs are redundant with other edges included in the networks (instead, CLN2 and CLB2 are used to represent canonical targets of TFs in the networks). Note 2. PLM2 is lacking specific literature evidence for its role as a TF activator. However, PLM2 is a paralog of TOS4 from the S. cerevisiae whole-genome duplication, and we propose that the activator function is shared between the paralogs. (XLSX 43 kb)